9AA-vs-DAN-optimization

Parameter Optimization Report

Project description: Comparison between DAN and 9AA matrices using HeLa cells (HeLa control and HeLa + 2DG). For 9AA:

  • methanol instead of ACN (the rest of parameters are the same as DAN)
  • mass spec is tuned based on glu, gln
  • laser focus was good
  • attn tuned to get good response

Date: 2022-10-23

Config: ./param_optimization/mans_opt_9AA_config.yml

Notebook version: 0.1

List of datasets

Optimization keys: ['Matrix']

Biological key: Treatment

Batch key: ['Matrix'] (data with different batch_keys will be processed separately)

  Unnamed: 0 Run Order Slide Position Matrix Slide Replicate Cell Line Treatment datasetId Problems mask Batch generated-replicate-name
0 0 1 C7 DAN 1 HeLa 2DG 2022-10-13_15h14m23s nan 0 DAN 1-C7
1 1 2 D2 DAN 1 NIH Control 2022-10-13_15h17m59s nan 1 DAN 1-D2
2 2 3 B5 DAN 1 HeLa Control 2022-10-13_14h55m13s nan 0 DAN 1-B5
3 3 4 B7 DAN 1 HeLa 2DG 2022-10-13_15h06m50s nan 0 DAN 1-B7
4 4 5 C4 DAN 1 NIH 2DG 2022-10-13_15h08m06s nan 1 DAN 1-C4
5 5 6 A3 DAN 1 NIH 2DG 2022-10-13_14h43m00s nan 1 DAN 1-A3
6 6 7 A6 DAN 1 HeLa Control 2022-10-13_14h44m58s nan 0 DAN 1-A6
7 7 8 D7 DAN 1 HeLa 2DG 2022-10-13_15h22m42s nan 0 DAN 1-D7
8 8 9 B2 DAN 1 NIH Control 2022-10-13_14h52m47s nan 1 DAN 1-B2
9 9 10 D3 DAN 1 NIH 2DG 2022-10-13_15h19m13s nan 1 DAN 1-D3
10 10 11 C6 DAN 1 HeLa Control 2022-10-13_15h10m58s Wrong focus 0 DAN 1-C6
11 11 12 A2 DAN 1 NIH Control 2022-10-13_14h39m04s Only 1/3 finished (instrument crash) 1 DAN 1-A2
12 12 13 nan DAN 1 nan Control 2022-10-13_15h26m35s Blank 1 DAN 1-nan
13 13 14 C8 9AA 2 HeLa 2DG 2022-10-14_15h42m22s nan 0 9AA 2-C8
14 14 15 D4 9AA 2 NIH 2DG 2022-10-14_15h43m59s nan 1 9AA 2-D4
15 15 16 D8 9AA 2 HeLa 2DG 2022-10-14_15h49m41s nan 0 9AA 2-D8
16 16 17 A2 9AA 2 NIH Control 2022-10-14_15h32m08s nan 1 9AA 2-A2
17 17 18 C3 9AA 2 NIH 2DG 2022-10-14_15h39m03s nan 1 9AA 2-C3
18 18 19 A3 9AA 2 NIH 2DG 2022-10-14_15h33m40s nan 1 9AA 2-A3
19 19 20 D6 9AA 2 HeLa Control 2022-10-14_15h46m09s nan 0 9AA 2-D6
20 20 21 B6 9AA 2 HeLa Control 2022-10-14_15h34m36s nan 0 9AA 2-B6
21 21 22 C1 9AA 2 NIH Control 2022-10-14_15h36m37s nan 1 9AA 2-C1
22 22 23 D7 9AA 2 HeLa 2DG 2022-10-14_15h47m35s nan 0 9AA 2-D7
23 23 24 C6 9AA 2 HeLa Control 2022-10-14_15h40m19s nan 0 9AA 2-C6
24 24 25 C2 9AA 2 NIH Control 2022-10-14_15h37m31s nan 1 9AA 2-C2
25 25 26 A7 DAN 3 HeLa 2DG 2022-10-14_16h01m07s nan 0 DAN 3-A7
26 26 27 B5 DAN 3 HeLa Control 2022-10-14_16h04m39s nan 0 DAN 3-B5
27 27 28 C6 DAN 3 HeLa Control 2022-10-14_16h08m17s nan 0 DAN 3-C6
28 28 29 D8 DAN 3 HeLa 2DG 2022-10-14_16h11m10s nan 0 DAN 3-D8
29 29 30 A7 9AA 4 HeLa 2DG 2022-10-14_17h40m40s nan 0 9AA 4-A7
30 30 31 B5 9AA 4 HeLa Control 2022-10-14_17h42m08s nan 0 9AA 4-B5
31 31 32 nan 9AA 4 nan Control 2022-10-14_19h28m32s Blank 1 9AA 4-nan
'datasetId'

Replicate coverage


PCA pixel analysis

When doing PCA and DE analysis, datasets belonging to the same batch are loaded together using an 'inner join': in other words, we only keep metabolites/annotations that are present in ALL datasets of a given batch. This is done to avoid artifacts in PCA analysis and volcano plots.

In general, keep in mind the following points:

  • PCA distances between conditions and replicates are comparable for datasets belonging to the same batch. Thus, you should try to put as many datasets as you can in the same batch.
  • However, when annotations of certain datasets are very different (e.g. because you acquired the data using different matrices), then you should consider putting them in a separate batch. Otherwise, not many common metabolites will be left after the 'inner join' done during loading.
  • If you notice that not many metabolites are left, then you could consider defining different batches or creating a custom database (see more info here)

Number of intra-cell pixels and ions left after loading (before and after filtering):

  Batch Unique pixels Unique ions
0 9AA 5120/5120 134/134
1 DAN 6401/6401 198/198

PCA plots

PCA distances

Intra-label vs. inter-label distance

The size of the circles represents PCA distances (the bigger the circle, the larger the distance):

  • The size of the colored circles represents the distance between the two biological conditions
  • The size of the empty circle with solid contour represents the distance between replicates of Control. If the circle is not present, it means that there was only one replicate available
  • The size of the empty circle with dotted contour represents the distance between replicates of 2DG. If the circle is not present, it means there was only one replicate available
  • You should only compare the size of circles with the same color (i.e. in the same batch), because PCA distances are not comparable between batches.

The best scenario is when both empty circles are inside the colored circle (i.e. the difference between replicates is smaller as compared to the difference between biological conditions).


Differential analysis and volcano plots


Markers intensities:

To show marker intensities, all datasets are loaded again using an 'outer' join: in other words, all annotations/metabolites that appear at least in one dataset are preserved; and if a metabolite is missing in some of the datasets, its intensity will be set to zero.

Markers found in at least one of the datasets (in alphabetical order):

  Marker name Formula and link to plots
0 AMP C10H14N5O7P+Cl
1 AMP C10H14N5O7P-H
2 Adenine C5H5N5-H
3 Glutathione C10H17N3O6S+Cl
4 Glutathione C10H17N3O6S-H
5 Guanine C5H5N5O-H
6 Uracil C4H4N2O2-H
7 aspartate C4H7NO4-H
8 aspartate C4H7NO4+Cl
9 citrate C6H8O7-H
10 fructose-bisphosphate C6H14O12P2-H
11 fumarate C4H4O4-H
12 fumarate C4H4O4+Cl
13 glucose C6H12O6-H
14 glucose C6H12O6+Cl
15 glucose-phosphate C6H13O9P-H
16 glutamate C5H9NO4-H
17 glutamate C5H9NO4+Cl
18 malate C4H6O5+Cl
19 malate C4H6O5-H
20 oleate C18H34O2-H
21 palmitate C16H32O2-H
22 succinate C4H6O4-H
23 succinate C4H6O4+Cl
24 taurine C2H7NO3S+Cl
25 taurine C2H7NO3S-H
26 threonine C4H9NO3+Cl
27 threonine C4H9NO3-H

Marker: C10H14N5O7P+Cl, AMP

Raw intensities (C10H14N5O7P+Cl, AMP)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H14N5O7P+Cl, AMP)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H14N5O7P+Cl, AMP)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C10H14N5O7P-H, AMP

Raw intensities (C10H14N5O7P-H, AMP)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H14N5O7P-H, AMP)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H14N5O7P-H, AMP)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C5H5N5-H, Adenine

Raw intensities (C5H5N5-H, Adenine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H5N5-H, Adenine)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H5N5-H, Adenine)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C10H17N3O6S+Cl, Glutathione

Raw intensities (C10H17N3O6S+Cl, Glutathione)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H17N3O6S+Cl, Glutathione)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H17N3O6S+Cl, Glutathione)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C10H17N3O6S-H, Glutathione

Raw intensities (C10H17N3O6S-H, Glutathione)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C10H17N3O6S-H, Glutathione)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C10H17N3O6S-H, Glutathione)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C5H5N5O-H, Guanine

Raw intensities (C5H5N5O-H, Guanine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H5N5O-H, Guanine)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H5N5O-H, Guanine)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H4N2O2-H, Uracil

Raw intensities (C4H4N2O2-H, Uracil)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H4N2O2-H, Uracil)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H4N2O2-H, Uracil)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H7NO4-H, aspartate

Raw intensities (C4H7NO4-H, aspartate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H7NO4-H, aspartate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H7NO4-H, aspartate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H7NO4+Cl, aspartate

Raw intensities (C4H7NO4+Cl, aspartate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H7NO4+Cl, aspartate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H7NO4+Cl, aspartate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C6H8O7-H, citrate

Raw intensities (C6H8O7-H, citrate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H8O7-H, citrate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H8O7-H, citrate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C6H14O12P2-H, fructose-bisphosphate

Raw intensities (C6H14O12P2-H, fructose-bisphosphate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H14O12P2-H, fructose-bisphosphate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H14O12P2-H, fructose-bisphosphate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H4O4-H, fumarate

Raw intensities (C4H4O4-H, fumarate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H4O4-H, fumarate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H4O4-H, fumarate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H4O4+Cl, fumarate

Raw intensities (C4H4O4+Cl, fumarate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H4O4+Cl, fumarate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H4O4+Cl, fumarate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C6H12O6-H, glucose

Raw intensities (C6H12O6-H, glucose)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H12O6-H, glucose)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H12O6-H, glucose)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C6H12O6+Cl, glucose

Raw intensities (C6H12O6+Cl, glucose)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H12O6+Cl, glucose)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H12O6+Cl, glucose)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C6H13O9P-H, glucose-phosphate

Raw intensities (C6H13O9P-H, glucose-phosphate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C6H13O9P-H, glucose-phosphate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C6H13O9P-H, glucose-phosphate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C5H9NO4-H, glutamate

Raw intensities (C5H9NO4-H, glutamate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H9NO4-H, glutamate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H9NO4-H, glutamate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C5H9NO4+Cl, glutamate

Raw intensities (C5H9NO4+Cl, glutamate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C5H9NO4+Cl, glutamate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C5H9NO4+Cl, glutamate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H6O5+Cl, malate

Raw intensities (C4H6O5+Cl, malate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O5+Cl, malate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O5+Cl, malate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H6O5-H, malate

Raw intensities (C4H6O5-H, malate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O5-H, malate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O5-H, malate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C18H34O2-H, oleate

Raw intensities (C18H34O2-H, oleate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C18H34O2-H, oleate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C18H34O2-H, oleate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C16H32O2-H, palmitate

Raw intensities (C16H32O2-H, palmitate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C16H32O2-H, palmitate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C16H32O2-H, palmitate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H6O4-H, succinate

Raw intensities (C4H6O4-H, succinate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O4-H, succinate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O4-H, succinate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H6O4+Cl, succinate

Raw intensities (C4H6O4+Cl, succinate)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H6O4+Cl, succinate)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H6O4+Cl, succinate)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C2H7NO3S+Cl, taurine

Raw intensities (C2H7NO3S+Cl, taurine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C2H7NO3S+Cl, taurine)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C2H7NO3S+Cl, taurine)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C2H7NO3S-H, taurine

Raw intensities (C2H7NO3S-H, taurine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C2H7NO3S-H, taurine)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C2H7NO3S-H, taurine)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H9NO3+Cl, threonine

Raw intensities (C4H9NO3+Cl, threonine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H9NO3+Cl, threonine)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H9NO3+Cl, threonine)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:


Marker: C4H9NO3-H, threonine

Raw intensities (C4H9NO3-H, threonine)

The following plot shows the raw intensities of intra-cellular pixels:

95% percentile (C4H9NO3-H, threonine)

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:

Detectability (C4H9NO3-H, threonine)

Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).

In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):

In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets: